source: branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp @ 512

Last change on this file since 512 was 512, checked in by mbayer, 14 years ago
  • have tied the interface to the importer plugin class now -- all parameters get picked up fine by the plugin
File size: 8.2 KB
Line 
1<%@ page import="net.sf.basedb.core.*"%>
2<%@ page import="net.sf.basedb.clients.web.*"%>
3<%@ page import="net.sf.basedb.util.*"%>
4<%@ page import="java.util.*"%>
5
6<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
7<!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
8<jsp:setProperty name="inputDataBean" property="*" />
9
10
11<html>
12<head>
13<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
14</head>
15<body>
16
17
18<%
19final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
20final String ID = sc.getId();
21final String requestID = request.getParameter("requestId");
22 %>
23
24<h2>Tab2MAGE Importer -- Your Hybridizations</h2>
25Page 3 of 3
26<p>
27<form action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
28<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters"> 
29<input type="hidden"name="requestID" value="<%=requestID%>"> 
30<!-- these are the parameters from the input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way -->
31<input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>"> 
32<input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>"> 
33<input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>"> 
34<input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>"> 
35<input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>"> 
36<input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>"> 
37<input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>"> 
38<input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>"> 
39<input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>"> 
40<input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>"> 
41<input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>"> 
42<input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>"> 
43<input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>"> 
44<input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>"> 
45<input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>"> 
46<input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>"> 
47<input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>"> 
48<input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>"> 
49<input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>"> 
50<input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>"> 
51<input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>"> 
52<input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>"> 
53<input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>"> 
54<input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>"> 
55<input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>"> 
56<input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>"> 
57<input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>"> 
58<input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>"> 
59
60<!-- 
61<input type="hidden" name="parameter:platform" value="<%=inputDataBean.getPlatform()%>">
62<input type="hidden" name="parameter:organism" value="<%=inputDataBean.getOrganism()%>">
63<input type="hidden" name="parameter:numDesigns" value="<%=inputDataBean.getNumDesigns()%>">
64<input type="hidden" name="parameter:dyeSwap" value="<%=inputDataBean.getDyeSwap()%>">
65<input type="hidden" name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>">
66<input type="hidden" name="parameter:numTreatments" value="<%=inputDataBean.getNumTreatments()%>">
67<input type="hidden" name="parameter:expFactors" value="<%=inputDataBean.getExpFactors()%>">
68<input type="hidden" name="parameter:numReplicates" value="<%=inputDataBean.getNumReplicates()%>">
69<input type="hidden" name="parameter:tissues" value="<%=inputDataBean.getTissues()%>">
70<input type="hidden" name="parameter:pooling" value="<%=inputDataBean.getPooling()%>">
71<input type="hidden" name="parameter:zipFile" value="<%=inputDataBean.getZipFile()%>">
72-->
73
74<!--  table with the input form -->
75<table cellpadding="15">
76
77  <!-- question 1 -->
78  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
79    <td class="boldText">Microarray platform used:</td>
80    <td class="input"><select name="parameter:platform">
81    <option >Genepix</option>
82    <option >Affymetrix</option>
83    </select></td>
84  </tr>
85
86  <!-- question 2 -->
87  <tr>
88    <td class="boldText">Name of the experimental organism:</td>
89    <td class="input"><input type="text" size="60" name="parameter:organism" value="barley"/></td>
90  </tr>
91
92  <!-- question 3 -->
93  <tr>
94    <td class="boldText">Number of different arrays designs used:</td>
95    <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
96  </tr>
97
98  <!-- question 4 -->
99  <tr>
100    <td class="boldText">Was dye-swap used?</td>
101    <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
102      name="parameter:dyeSwap" value="no" checked="checked"> <br>
103    </td>
104  </tr>
105
106  <!-- question 5 -->
107  <tr>
108    <td class="boldText">Was a reference sample used?</td>
109    <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
110      name="parameter:refSample" value="no" checked="checked"></td>
111  </tr>
112
113  <!-- question 6 -->
114  <tr>
115    <td class="boldText">Number of treatments used:</td>
116    <td class="input"><input type="text" size="3" name="parameter:numTreatments" value="2"/></td>
117  </tr>
118
119  <!-- question 7 -->
120  <tr>
121    <td class="boldText">Please list your experimental factors and value ranges using the following format (one per
122    line):<br>
123    <i>Factor 1(value1,value2,...valueN)<br>
124    Factor 2(value1,value2,...valueN)</i>
125    <p>Example: <i><br>
126    Compound(aspirin,ibuprofen,acetaminophen) <br>
127    Dose(control,low,medium,high)</i>
128    </td>
129    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Factor 1(value1,value2,...valueN)</textarea></td>
130  </tr>
131
132  <!-- question 8 -->
133  <tr>
134    <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>
135    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="3"/></td>
136  </tr>
137 
138  <!-- question 9 -->
139  <tr>
140    <td class="boldText">List all target tissues (as a comma separated list).<br>
141    Example: liver,heart,adipose tissue</td>
142    <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">tissues1,tissue2</textarea></td>
143  </tr>
144 
145  <!-- question 10 -->
146  <tr>
147    <td class="boldText">Were samples pooled?</td>
148    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
149      name="parameter:pooling" value="no" checked="checked"></td>
150  </tr>
151
152
153  <!-- file upload -->
154  <tr>
155    <td class="boldText">Please select the zip file on your local disk that contains the data files for import:</td>
156    <td class="input"><INPUT type="file" name="parameter:zipFile" size="50" value="test.txt"></td>
157  </tr>
158
159</table>
160
161<p>
162<table class="noBorder" width="100%">
163  <tr class="noBorder">
164    <td class="centered"><input type="submit" value="Run Import" /></td>
165  </tr>
166</table>
167
168
169</form>
170
171</body>
172</html>
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